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Table 4 Comparison of MAIA and GP spot filtering approaches on a set of 24 selected genes confirmed by RT-PCR or qRT-PCR.

From: Advanced spot quality analysis in two-colour microarray experiments

Symbol Description MAIA GP-standard GP-weak GP-medium GP-strong
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KLF5 Krueppel-like factor 5 + + + +  
TJP3 Tight junction protein ZO-3 + + +   
KRT12 Keratin, type I cytoskeletal 12 + + +   
BSPRY B-box and SPRY domain containing +   +   
CORO1A Coronin-1A + + + +  
STAP2_HUMAN Signal-transducing adaptor protein 2 +   +   
PPP1R16A Protein phosphatase 1 regulatory subunit 16A + + + + +
KRT18 Keratin, type I cytoskeletal 18 +     
STMN3 Stathmin-3 + + + +  
TRIB3 Tribbles homolog 3 +   +   
CLDN3 Claudin-3 +     
TXNIP Thioredoxin interacting protein +     
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MSX1 Homeobox protein MSX-1 + + + +  
GULP1 GULP, engulfment adaptor PTB domain containing 1 + + + +  
DUSP2 Dual specificity protein phosphatase 2 + + + +  
ID3 DNA-binding protein inhibitor ID-3 +     
THBD Thrombomodulin precursor + + +   
HS6ST2 Heparan sulfate 6-O-sulfotransferase 2 + + +   
TGFBI Transforming growth factor-beta-induced protein ig-h3 precursor +     
S 100A 10 Calpactin I light chain +     
SERPINH1 Collagen-binding protein 2 precursor +     
SNAI2 Zinc finger protein SLUG + + +   
COL5A1 Collagen alpha 1(V) chain precursor + + + +  
ANXA2 Annexin A2 + + + + +
  1. RT-PCR and qRT-PCR analysis of 24 selected genes was performed to validate microarray data. Then, the presence of these genes in lists of DE genes obtained in the whole-genome microarray experiment was determined using different spot quality evaluation approaches in MAIA and GP. Fourteen genes were detected using the GP-standard conditions, 17, 9, 2 were present in the GP-weak, GP-medium, GP-strong lists, correspondingly. All 24 genes were found in the MAIA DE gene list. The sign "+" indicates if a gene is present in the corresponding DE gene list.